RT Journal Article SR Electronic T1 Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing JF bioRxiv FD Cold Spring Harbor Laboratory SP 2020.09.11.292656 DO 10.1101/2020.09.11.292656 A1 Aleksandra Bliznina A1 Aki Masunaga A1 Michael J. Mansfield A1 Yongkai Tan A1 Andrew W. Liu A1 Charlotte West A1 Tanmay Rustagi A1 Hsiao-Chiao Chien A1 Saurabh Kumar A1 Julien Pichon A1 Charles Plessy A1 Nicholas M. Luscombe YR 2020 UL http://biorxiv.org/content/early/2020/09/12/2020.09.11.292656.abstract AB Background The larvacean Oikopleura dioica is an abundant tunicate plankton with the smallest (65-70 Mbp) non-parasitic, non-extremophile animal genome identified to date. Currently, there are two genomes available for the Bergen (OdB3) and Osaka (OSKA2016) O. dioica laboratory strains. Both assemblies have full genome coverage and high sequence accuracy. However, a chromosome-scale assembly has not yet been achieved.Results Here, we present a chromosome-scale genome assembly (OKI2018_I69) of the Okinawan O. dioica produced using long-read Nanopore and short-read Illumina sequencing data from a single male, combined with Hi-C chromosomal conformation capture data for scaffolding. The OKI2018_I69 assembly has a total length of 64.3 Mbp distributed among 19 scaffolds. 99% of the assembly is in five megabase-scale scaffolds. We found telomeres on both ends of the two largest scaffolds, which represent assemblies of two fully contiguous autosomal chromosomes. Each of the other three large scaffolds have telomeres at one end only and we propose that they correspond to sex chromosomes split into a pseudo-autosomal region and X-specific or Y-specific regions. Indeed, these five scaffolds mostly correspond to equivalent linkage groups of OdB3, suggesting overall agreement in chromosomal organization between the two populations. At a more detailed level, the OKI2018_I69 assembly possesses similar genomic features in gene content and repetitive elements reported for OdB3. The Hi-C map suggests few reciprocal interactions between chromosome arms. At the sequence level, multiple genomic features such as GC content and repetitive elements are distributed differently along the short and long arms of the same chromosome.Conclusions We show that a hybrid approach of integrating multiple sequencing technologies with chromosome conformation information results in an accurate de novo chromosome-scale assembly of O. dioica’s highly polymorphic genome. This assembly will be a useful resource for genome-wide comparative studies between O. dioica and other species, as well as studies of chromosomal evolution in this lineage.Competing Interest StatementThe authors have declared no competing interest.chr 1autosomal chromosome 1chr 2autosomal chromosome 2KbpKilobase pairsLGslinkage groupsMbpMegabase pairsPARpseudo-autosomal regionsXSRX-specific regionYSRY-specific region